Functional characterization of somatic mutations in cancer using network-based inference of protein activity

Interrogation of a Context-Specific Transcription Factor Network Identifies Novel Regulators of Pluripotency

(2015) Ritu Kushwaha et al.   STEM CELLS

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Cross-Species Regulatory Network Analysis Identifies a Synergistic Interaction between FOXM1 and CENPF that Drives Prostate Cancer Malignancy

(2014) Alvaro Aytes et al.   CANCER CELL

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

(2014) James C. Chen et al.   CELL

Prospective Enterprise-Level Molecular Genotyping of a Cohort of Cancer Patients

(2014) Laura E. MacConaill et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Interplay between nuclear transport and ubiquitin/SUMO modifications in the regulation of cancer-related proteins

(2014) Jose A. Rodríguez   SEMINARS IN CANCER BIOLOGY

Control of mRNA turnover: Implication of cytoplasmic RNA granules

(2014) Pauline Adjibade et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State

(2014) Yakov Chudnovsky et al.   Cell Reports

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia

(2013) Erich Piovan et al.   CANCER CELL

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules

(2013) Amrita Basu et al.   CELL

Molecular Pathways: SWI/SNF (BAF) Complexes Are Frequently Mutated in Cancer--Mechanisms and Potential Therapeutic Insights

(2013) X. Wang et al.   CLINICAL CANCER RESEARCH

Quantitative mass spectrometry-based assay development and validation: From small molecules to proteins

(2012) Andrea Božović et al.   CLINICAL BIOCHEMISTRY

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

A Comprehensive Statistical Model for Cell Signaling

(2010) E Yoruk et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype

(2010) So Yeon Park et al.   JOURNAL OF CLINICAL INVESTIGATION

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells

(2009) K. Basso et al.   BLOOD

Comparative study of gene set enrichment methods

(2009) Luca Abatangelo et al.   BMC BIOINFORMATICS

Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction

(2009) Ji Luo et al.   CELL

Dissecting protein function and signaling using protein microarrays

(2009) Alejandro Wolf-Yadlin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Mutations of multiple genes cause deregulation of NF-κB in diffuse large B-cell lymphoma

(2009) Mara Compagno et al.   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Residual breast cancers after conventional therapy display mesenchymal as well as tumor-initiating features

(2009) C. J. Creighton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlating measurements across samples improves accuracy of large-scale expression profile experiments

(2009) Mariano Alvarez et al.   GENOME BIOLOGY

Novel Molecular Subtypes of Serous and Endometrioid Ovarian Cancer Linked to Clinical Outcome

(2008) R. W. Tothill et al.   CLINICAL CANCER RESEARCH

Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

(2008) André Boorsma et al.   PLoS One

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology